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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Micro-Analyzer Resource Report Resource Website |
Micro-Analyzer (RRID:SCR_000394) | Micro-Analyzer | software resource | Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems. | windows, linux, java, java swing, gene expression, snp, microarray, affymetrix, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23731720 | Free, Available for download, Freely available | OMICS_01919, biotools:microanalyzer | https://bio.tools/microanalyzer | SCR_000394 | microAnalyzer | 2026-02-14 01:59:43 | 0 | |||||
|
SAMBLASTER Resource Report Resource Website 10+ mentions |
SAMBLASTER (RRID:SCR_000468) | software resource | Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Virginia; Virginia; USA |
PMID:24812344 DOI:10.1093/bioinformatics/btu314 |
Free, Available for download, Freely available | biotools:samblaster, OMICS_04682 | https://bio.tools/samblaster https://sources.debian.org/src/samblaster/ |
SCR_000468 | 2026-02-14 01:59:46 | 18 | |||||||
|
TAPyR Resource Report Resource Website 1+ mentions |
TAPyR (RRID:SCR_000588) | software resource | An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies. | gs flx, genome analyzer, bwt, fasta, fastq, sff formats, pyrosequencing reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21672185 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tapyr, OMICS_00693 | https://bio.tools/tapyr | SCR_000588 | Tool for Alignment of Pyrosequencing Reads | 2026-02-14 01:59:46 | 1 | ||||||
|
MuTect Resource Report Resource Website 50+ mentions |
MuTect (RRID:SCR_000559) | MuTect | software resource | Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. | next-generation sequencing, somatic mutation, tumor, normal, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Cancer | PMID:23396013 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mutect, OMICS_00087 | https://bio.tools/mutect | SCR_000559 | Mutect | 2026-02-14 01:59:45 | 91 | ||||
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SRMA Resource Report Resource Website |
SRMA (RRID:SCR_000669) | SRMA | software resource | A post-alignment micro re-aligner for next-generation high throughput sequencing data. | matlab, sequence re-alignment, command-line, java, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20932289 | Free, Available for download, Freely available | biotools:srma, OMICS_01079 | https://bio.tools/srma | SCR_000669 | Short Read Micro re-Aligner | 2026-02-14 01:59:47 | 0 | |||||
|
AffyRNADegradation Resource Report Resource Website |
AffyRNADegradation (RRID:SCR_000118) | AffyRNADegradation | software resource | Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation. | rna degradation, gene expression, microarray, preprocessing, affymetrix, rna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: University of Leipzig; Saxony; Germany |
PMID:23097420 | Free, Available for download, Freely available | OMICS_01975, biotools:affyrnadegradation | https://bio.tools/affyrnadegradation | SCR_000118 | 2026-02-14 01:59:37 | 0 | ||||||
|
SOAPfusion Resource Report Resource Website 1+ mentions |
SOAPfusion (RRID:SCR_000079) | SOAPfusion | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards. | software, open source, free, RNA, sequencing, data, computing, research, analysis, rna-seq, candidate regions, bio.tools |
is listed by: OMICtools is listed by: SOAP is listed by: bio.tools is listed by: Debian |
Guangdong Innovative Research Team Program ; General Research Fund of the Hong Kong Government |
PMID:24123671 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01358, biotools:soapfusion | https://bio.tools/soapfusion | SCR_000079 | 2026-02-14 01:59:36 | 3 | |||||
|
timecourse Resource Report Resource Website 1+ mentions |
timecourse (RRID:SCR_000077) | timecourse | software resource | Software functions for data analysis and graphical displays for developmental microarray time course data. | microarray, differential expression, time course, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: CRAN has parent organization: Bioconductor has parent organization: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | OMICS_01980, biotools:timecourse | https://bio.tools/timecourse | SCR_000077 | timecourse - Statistical Analysis for Developmental Microarray Time Course Data | 2026-02-14 01:59:36 | 5 | ||||||
|
Patchwork Resource Report Resource Website 1+ mentions |
Patchwork (RRID:SCR_000072) | Patchwork | software resource | Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data. | genome, allele, copy number, bam, unix, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Uppsala University; Uppsala; Sweden |
Cancer, Tumor | PMID:23531354 | Free, Available for download, Freely available | biotools:patchwork, OMICS_02118 | https://bio.tools/patchwork | SCR_000072 | 2026-02-14 01:59:36 | 9 | |||||
|
SNAVI Resource Report Resource Website |
SNAVI (RRID:SCR_000091) | software resource | Desktop application for analysis and visualization of large-scale cell signaling networks. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:19154595 | Free, Available for download, Freely available | biotools:snavi, OMICS_04122 | https://bio.tools/snavi | SCR_000091 | Signaling Networks Analysis and Visualization | 2026-02-14 01:59:37 | 0 | ||||||
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Phenoscape Resource Report Resource Website 1+ mentions |
Phenoscape (RRID:SCR_003799) | Phenoscape | data or information resource, portal | Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions. | phenotype, bio.tools |
is listed by: Debian is listed by: bio.tools is parent organization of: Teleost Anatomy Ontology is parent organization of: Vertebrate Taxonomy Ontology is parent organization of: Phenoscape Knowledgebase |
NSF DBI-1062404; NSF DBI-1062542; NSF BDI-0641025; NSF EF-0905606; NSF EF-0423641 |
biotools:Phenoscape, nlx_158096 | https://bio.tools/Phenoscape | SCR_003799 | 2026-02-14 02:05:03 | 8 | |||||||
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CATdb: a Complete Arabidopsis Transcriptome database Resource Report Resource Website 10+ mentions |
CATdb: a Complete Arabidopsis Transcriptome database (RRID:SCR_007582) | data or information resource, database | CATdb collects together all the information on transcriptome experiments done at URGV with CATMA micro arrays. All data in CATdb come from the URGV micro array platforms. Common procedures are used including any steps from the experiment design to the statistical analyses. Directed through a WEB interface, biologists enter the standard description of each experimental step (extraction, labelling, hybridization and scanning). Then, normalization and statistical analyses are done following a set of selected methods depending on the experimental design and array types. | catma, microarray, transcriptome, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Evry-Val d'Essonne; Ile-de-France; France |
nif-0000-02639, biotools:catdb | https://bio.tools/catdb | SCR_007582 | CATdb | 2026-02-14 02:06:29 | 40 | ||||||||
|
Allele Frequencies in Worldwide Populations Resource Report Resource Website 100+ mentions |
Allele Frequencies in Worldwide Populations (RRID:SCR_007259) | data or information resource, database | The main purpose of the allelefrequencies.net website is to provide one central source, freely available to all. For the storage of allele frequencies from different polymorphic areas in the HUMAN genome. Users can contribute the results of their work into one common database, and can perform database searches on information already available. They have currently collected data in allele, haplotype and genotype format. The success of this website will depend on you to contribute your data. Sponsors: This resource is supported Royal Liverpool University. Keywords: Allele, Polymorphic, Genome, Database, Data, Haplotype, Genotype, | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Royal Liverpool University; Liverpool; United Kingdom |
r3d100011904, biotools:allele_frequency_net, nif-0000-30079 | https://bio.tools/allele_frequency_net https://doi.org/10.17616/R3F063 |
SCR_007259 | Allele Frequencies | 2026-02-14 02:06:03 | 411 | ||||||||
|
Full-Length cDNA Database Resource Report Resource Website 1+ mentions |
Full-Length cDNA Database (RRID:SCR_007666) | data or information resource, database | Full-Length cDNA Database is a resource for cDNA libraries of arhtropods and parasites. The arthropod species covered are Anopheles stephensi, Glossina morsitans (Tsetse fly), and Dermatophagoides farinae (House dust mite), while the parasitic species included are Plasmodium falciparum (Malaria), Toxoplasma gondii, Cryptosporidium parvum, Babesia bovis (Babesia), and Echinococcus multilocularis. A specialized database of each species is available as a link from the home page. This database has been constructed and maintained since 2001 by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science. Anopheles stephensi, Glossina morsitans, Tsetse fly, Dermatophagoides farinae, House dust mite, Plasmodium falciparum, Malaria, Toxoplasma gondii, Cryptosporidium parvum, Babesia bovis, Babesia, Echinococcus multilocularis, cDNA, cDNA library, arthropod genome, parasite genome | echinococcus multilocularis, anopheles stephensi, arthropod genome, babesia, babesia bovis, cdna, cdna library, cryptosporidium parvum, dermatophagoides farinae, glossina morsitans, house dust mite, malaria, parasite genome, plasmodium falciparum, toxoplasma gondii, tsetse fly, bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:full-parasites, nif-0000-02856 | https://bio.tools/full-parasites | SCR_007666 | Full-Length cDNA Database | 2026-02-14 02:06:37 | 6 | ||||||||
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miROrtho: the catalogue of animal microRNA genes Resource Report Resource Website 1+ mentions |
miROrtho: the catalogue of animal microRNA genes (RRID:SCR_007797) | data or information resource, database | It contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline. The current release of miROrtho covers 46 animal genomes. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Geneva; Geneva; Switzerland |
nif-0000-03139, biotools:mirortho | https://bio.tools/mirortho | SCR_007797 | miROrtho | 2026-02-14 02:06:08 | 4 | ||||||||
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Noncoding RNA database Resource Report Resource Website 10+ mentions |
Noncoding RNA database (RRID:SCR_007815) | ncRNA | data or information resource, database | It is intended to provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell. Currently, the database includes over 30,000 individual sequences from 99 species of Bacteria, Archaea and Eukaryota. The primary source of sequences included in the database was the GenBank. Additional annotation information for mouse and human ncRNAs was derived from FANTOM3 database and H-inviational Integrated Database of Annotated Human Genes version 3.4, respectively. Genome mapping information was derived from tha data available at the UCSC Genome Browser site. The sequences and annotations of small cytoplasmic RNAs from bacteria, for which annotation is lacking in the genome sequences, were derived from the Rfam database. The microRNAs or snoRNAs which were available in previous editions, as well as other housekeeping (infrastructural) RNAs (e.g. rRNA, tRNA, snRNA, SRP RNA) are not included in our database to avoid redundancy with more specialized databases which emerged in recent years. | bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-03183, biotools:ncrna | https://bio.tools/ncrna | SCR_007815 | Noncoding RNA database | 2026-02-14 02:06:31 | 13 | |||||||
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IMG Resource Report Resource Website 500+ mentions |
IMG (RRID:SCR_007733) | IMG | data or information resource, database | Datasets and tools for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context. Plasmids that are not part of a specific microbial genome sequencing project and phage genomes are also included in order to increase its genomic context for comparative analysis. The user interface (see User Interface Map) allows navigating the microbial genome data space along its three key dimensions (genes, genomes, and functions), and groups together the main comparative analysis tools. Microbial genome data analysis in IMG usually starts with the definition of an analysis context in terms of selected genomes, functional annotations, and/or genes, followed by the individual or comparative analysis of genomes, functional annotations, or genes. | genome, microorganism, annotation, bio.tools, FASEB list |
is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: DOE Joint Genome Institute |
nif-0000-03009, biotools:img | https://bio.tools/img | SCR_007733 | Integrated Microbial Genomes | 2026-02-14 02:06:02 | 652 | |||||||
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MetaCyc Resource Report Resource Website 1000+ mentions |
MetaCyc (RRID:SCR_007778) | MetaCyc | data or information resource, database | MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1,200 pathways from more than 1,600 different organisms, and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes. | bio.tools, FASEB list |
uses: Pathway Tools is listed by: BioCyc is listed by: bio.tools is listed by: Debian is related to: BioCyc is related to: ENZYME is related to: NCBI BioSystems Database is related to: Algal Functional Annotation Tool is related to: Pathway Tools has parent organization: Stanford Research Institute International works with: MiMeDB |
r3d100011294, nif-0000-03114, biotools:metacyc | https://bio.tools/metacyc https://doi.org/10.17616/R32K7X |
SCR_007778 | 2026-02-14 02:06:31 | 1761 | ||||||||
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MEROPS Resource Report Resource Website 500+ mentions |
MEROPS (RRID:SCR_007777) | MEROPS, MEROPS fam | data or information resource, database | An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more. | peptidase, protease, proteinase, proteolytic enzyme, protein, inhibitor, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: TopFIND has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT077044/Z/05/Z | PMID:19892822 | biotools:merops, r3d100012783, nif-0000-03112 | https://bio.tools/merops https://doi.org/10.17616/R33225 https://doi.org/10.17616/R33225 |
SCR_007777 | MEROPS- the Peptidase Database, MEROPS - the Peptidase Database, MEROPS database, MEROPS fam | 2026-02-14 02:06:03 | 736 | |||||
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LOCATE: subcellular localization database Resource Report Resource Website 50+ mentions |
LOCATE: subcellular localization database (RRID:SCR_007763) | data or information resource, database | LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set. The membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing peer-reviewed publications. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Queensland; Brisbane; Australia |
nif-0000-03086, biotools:locate | https://bio.tools/locate | SCR_007763 | LOCATE | 2026-02-14 02:06:38 | 66 |
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